Abstract: In this paper we present a technique for interactively rendering transparent molecular surfaces. We use Puxels, our implementation of per-pixel linked lists for order-independent transparency rendering. Furthermore, we evaluate the usage of per-pixel arrays as an alternative for this rendering technique. We describe our real-time rendering technique for transparent depiction of complex molecular surfaces like the Solvent Excluded Surface which is based on constructive solid geometry. Additionally, we explain further graphical operations and extensions possible with the Puxels approach. The evaluation benchmarks the performance of the presented methods and compares it to other methods.